Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008613.1 Hibiscus syriacus cultivar Beakdansim tig00111569_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 647085
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:673 original size:14 final size:14
Alignment explanation
Indices: 650--679 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
640 TTACTTTGAG
650 TTTCTCAATAAAAC
1 TTTCTCAATAAAAC
*
664 TTTCTTAATAAAAC
1 TTTCTCAATAAAAC
678 TT
1 TT
680 AAAAGATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCTCAATAAAAC
Found at i:4636 original size:32 final size:32
Alignment explanation
Indices: 4588--4666 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
4578 CACTTGATTT
4588 GATATTGACCCGACCC-AAAATCTAACCGATCC
1 GATATTGACCCGACCCAAAAATC-AACCGATCC
* * *
4620 GGTATTAACCCGACCCAAAAATCAACTGATCC
1 GATATTGACCCGACCCAAAAATCAACCGATCC
*
4652 GACATTGACCCGACC
1 GATATTGACCCGACC
4667 TGATATTGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 34 0.85
33 6 0.15
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (32 bp):
GATATTGACCCGACCCAAAAATCAACCGATCC
Found at i:8246 original size:19 final size:20
Alignment explanation
Indices: 8201--8254 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
8191 AACTACAAGG
* *
8201 AAAGTTTTAAAACTCTTGTT
1 AAAGTTTTGAAACTCTAGTT
8221 AAAGTTTTGAAACTCTAG-T
1 AAAGTTTTGAAACTCTAGTT
* *
8240 GAAGTTTCGAAACTC
1 AAAGTTTTGAAACTC
8255 CAAAGTCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (20 bp):
AAAGTTTTGAAACTCTAGTT
Found at i:9648 original size:16 final size:17
Alignment explanation
Indices: 9616--9651 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
9606 TTTGTTTTTT
9616 AAAATCAAACTTTATTTC
1 AAAATCAAAC-TTATTTC
9634 AAAATCAAA-TTATTTC
1 AAAATCAAACTTATTTC
9650 AA
1 AA
9652 CTTTGAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATCAAACTTATTTC
Found at i:10827 original size:28 final size:28
Alignment explanation
Indices: 10761--10922 Score: 162
Period size: 29 Copynumber: 5.7 Consensus size: 28
10751 AATTGTTGTT
* * *
10761 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGACATTTTGGGAATTATTTCGA-AA
*
10790 AGGTGACATTTTGGGAATTATTTTGAAA
1 AGGTGACATTTTGGGAATTATTTCGAAA
* * * *
10818 AGATGACATTATGGGAAATATTTCAAAA
1 AGGTGACATTTTGGGAATTATTTCGAAA
* *
10846 AGGTAACATATTGGGAATTATTTCGTAAA
1 AGGTGACATTTTGGGAATTATTTCG-AAA
* * **
10875 AGGTGACACTCTGGGAATTATTTTAAAAA
1 AGGTGACATTTTGGGAATTA-TTTCGAAA
*
10904 AAGTGACATTTTGGGAATT
1 AGGTGACATTTTGGGAATT
10923 TTCAAATGTT
Statistics
Matches: 107, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
28 44 0.41
29 60 0.56
30 3 0.03
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (28 bp):
AGGTGACATTTTGGGAATTATTTCGAAA
Found at i:10877 original size:85 final size:84
Alignment explanation
Indices: 10772--10928 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 84
10762 GGTGATATTC
* * * *
10772 TGGGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTGAAAAGA-TGACATTATGGGAAA
1 TGGGAAATATTTCGATAAAGGTGACACTCTGGGAATTATTTTAAAAAAAGTGACATTATGGG-AA
10836 TATTTCAAAAAGGTAACATAT
65 T-TTTCAAAAAGGTAACATAT
* *
10857 TGGGAATTATTTCG-TAAAAGGTGACACTCTGGGAATTATTTTAAAAAAAGTGACATTTTGGGAA
1 TGGGAAATATTTCGAT-AAAGGTGACACTCTGGGAATTATTTTAAAAAAAGTGACATTATGGGAA
10921 TTTTCAAA
65 TTTTCAAA
10929 TGTTTGACAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
84 8 0.12
85 45 0.70
86 11 0.17
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (84 bp):
TGGGAAATATTTCGATAAAGGTGACACTCTGGGAATTATTTTAAAAAAAGTGACATTATGGGAAT
TTTCAAAAAGGTAACATAT
Found at i:11759 original size:22 final size:23
Alignment explanation
Indices: 11734--11781 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
11724 CTTAGGGTAA
11734 GCTATATGGACTTA-TGACTTGG
1 GCTATATGGACTTATTGACTTGG
11756 GCTATATGGACTTATTGACTTGG
1 GCTATATGGACTTATTGACTTGG
11779 GCT
1 GCT
11782 TAAGGATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.38
Consensus pattern (23 bp):
GCTATATGGACTTATTGACTTGG
Found at i:17429 original size:29 final size:29
Alignment explanation
Indices: 17376--17526 Score: 119
Period size: 29 Copynumber: 5.3 Consensus size: 29
17366 GGTTATATTC
* * **
17376 TGGGAAATATTTCGATAAAGGTGACATTT
1 TGGGAATTATTTCGAAAAAAATGACATTT
* *
17405 TGGGAATTATTTTGAAAAAAATGACATTA
1 TGGGAATTATTTCGAAAAAAATGACATTT
* * * * *
17434 TGGGAAATATGTCG--AAAAGTAACATAT
1 TGGGAATTATTTCGAAAAAAATGACATTT
* ** * *
17461 TGGGAATTATTTCGTAAAAGGTGACACTC
1 TGGGAATTATTTCGAAAAAAATGACATTT
*
17490 TGGGAATTATTT-TAAAAAAAGTGACATTT
1 TGGGAATTATTTCGAAAAAAA-TGACATTT
17519 TGGGAATT
1 TGGGAATT
17527 TTCAAATGTT
Statistics
Matches: 93, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
27 21 0.23
28 4 0.04
29 68 0.73
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (29 bp):
TGGGAATTATTTCGAAAAAAATGACATTT
Found at i:17486 original size:56 final size:58
Alignment explanation
Indices: 17376--17495 Score: 145
Period size: 56 Copynumber: 2.1 Consensus size: 58
17366 GGTTATATTC
* * * * *
17376 TGGGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTGAAAAAAATGACATTA
1 TGGGAAATATGTCGATAAAGGTAACATATTGGGAATTATTTCGAAAAAAATGACACTA
* ** *
17434 TGGGAAATATGTCGA-AAA-GTAACATATTGGGAATTATTTCGTAAAAGGTGACACTC
1 TGGGAAATATGTCGATAAAGGTAACATATTGGGAATTATTTCGAAAAAAATGACACTA
17490 TGGGAA
1 TGGGAA
17496 TTATTTTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 36 0.68
57 3 0.06
58 14 0.26
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (58 bp):
TGGGAAATATGTCGATAAAGGTAACATATTGGGAATTATTTCGAAAAAAATGACACTA
Found at i:19957 original size:20 final size:19
Alignment explanation
Indices: 19932--19977 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
19922 AAAGTTTTTT
*
19932 GAAACTCTTGTCAAAGTTTC
1 GAAACTCTAGT-AAAGTTTC
* *
19952 GAAACTCTAGTGAAGTTTT
1 GAAACTCTAGTAAAGTTTC
19971 GAAACTC
1 GAAACTC
19978 CAAAGCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (19 bp):
GAAACTCTAGTAAAGTTTC
Found at i:25575 original size:21 final size:21
Alignment explanation
Indices: 25524--25576 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
25514 ATTATAACTA
25524 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
25545 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
25566 TCGCAATGCGA
1 TCGCAATGCGA
25577 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:25689 original size:20 final size:20
Alignment explanation
Indices: 25566--25697 Score: 160
Period size: 20 Copynumber: 6.5 Consensus size: 20
25556 TTTTCCCAAT
*
25566 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
25586 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
25606 TCGCAACGCG-ATAAAGTAAA
1 TCGCAATGCGAAT-ACGTAAA
* *
25626 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
25647 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
25667 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
25687 TCGCAATGCGA
1 TCGCAATGCGA
25698 TTTATATAGC
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
19 5 0.05
20 74 0.76
21 18 0.18
22 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:26274 original size:19 final size:19
Alignment explanation
Indices: 26252--26296 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
26242 GCAACGAGAG
*
26252 AATCGCAACGCAAAATAAA
1 AATCGCAACGCAAAACAAA
* *
26271 AATCGCAACGCGAAACCAA
1 AATCGCAACGCAAAACAAA
26290 AATCGCA
1 AATCGCA
26297 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.27, G:0.13, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCAAAACAAA
Found at i:26314 original size:19 final size:19
Alignment explanation
Indices: 26292--26470 Score: 118
Period size: 19 Copynumber: 10.1 Consensus size: 19
26282 GAAACCAAAA
*
26292 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
26311 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
26325 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
26344 TTGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
26363 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
26377 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* * *
26396 TCGCATTGTGATTCTC--T
1 TCGCGTTGCGATTTTCATT
**
26413 T---GTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
26429 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
26449 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
26469 TC
1 TC
26471 AACCAAAAGA
Statistics
Matches: 123, Mismatches: 20, Indels: 34
0.69 0.11 0.19
Matches are distributed among these distances:
14 28 0.23
16 7 0.06
17 8 0.07
19 50 0.41
20 29 0.24
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:26384 original size:33 final size:33
Alignment explanation
Indices: 26347--26445 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
26337 TTTCATTTTG
**
26347 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
* *
26380 CGTTGCGATAGTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
26413 TGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
26446 ATTATCTCGT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:26395 original size:52 final size:52
Alignment explanation
Indices: 26297--26396 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
26287 CAAAATCGCA
**
26297 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTTGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTTGCG
26349 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTT
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTT
26397 CGCATTGTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTTGCG
Found at i:26447 original size:20 final size:20
Alignment explanation
Indices: 26414--26470 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
26404 TGATTCTCTT
**
26414 GTTGCGATAGTCATTTCCGC
1 GTTGCGATTCTCATTTCCGC
*
26434 GTTGCGATTCTCATTAT-CTC
1 GTTGCGATTCTCATT-TCCGC
*
26454 GTTGCGATTTTCATTTC
1 GTTGCGATTCTCATTTC
26471 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
GTTGCGATTCTCATTTCCGC
Found at i:28640 original size:21 final size:21
Alignment explanation
Indices: 28616--28682 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
28606 TCATTCCTCG
28616 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
28637 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
28658 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
28679 AGAG
1 AGAG
28683 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:28640 original size:42 final size:41
Alignment explanation
Indices: 28569--28682 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
28559 GCCTGTTATC
* * * * * *
28569 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-T
*
28611 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCAT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
* * *
28652 CGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
28683 CCCGATTCAC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.07
42 54 0.90
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (41 bp):
CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
Found at i:30052 original size:14 final size:14
Alignment explanation
Indices: 30033--30068 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
30023 ATTGTTTAAT
30033 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
30047 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
30061 TGATTTGT
1 TGATTTGT
30069 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:30212 original size:14 final size:14
Alignment explanation
Indices: 30193--30249 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
30183 GCGAAATGAA
30193 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
30207 AATCGCAACACAAAATGAA
1 AATCGC-A-AC--GA-GAG
30226 AATCGCAACGAGAG
1 AATCGCAACGAGAG
30240 AATCGCAACG
1 AATCGCAACG
30250 CGAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 8 0.24
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:30223 original size:33 final size:33
Alignment explanation
Indices: 30186--30248 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
30176 TCGCAATGCG
30186 AAATGAAAATCGCAACGAGAGAATCGCAACACA
1 AAATGAAAATCGCAACGAGAGAATCGCAACACA
30219 AAATGAAAATCGCAACGAGAGAATCGCAAC
1 AAATGAAAATCGCAACGAGAGAATCGCAAC
30249 GCGAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACACA
Found at i:30307 original size:33 final size:31
Alignment explanation
Indices: 30259--30424 Score: 170
Period size: 33 Copynumber: 5.1 Consensus size: 31
30249 GCGAAATTAA
* *
30259 ATTCGTGTTGCGATTTTTATTTCGCATTGCG
1 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
30290 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCAAA
1 ATT--CGCGTTGCGATTTTCATTTCGCATTGC--G
30325 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
30356 AAATTCGCATTGCGATTTTCATTTCGCATTGCG
1 --ATTCGCGTTGCGATTTTCATTTCGCATTGCG
* ** *
30389 ATTCTCTCGTTGCGATAGTAATTTCCGCATTGCG
1 A-T-TCGCGTTGCGATTTTCATTT-CGCATTGCG
30423 AT
1 AT
30425 AGACATTAAG
Statistics
Matches: 114, Mismatches: 12, Indels: 16
0.80 0.08 0.11
Matches are distributed among these distances:
31 4 0.04
32 1 0.01
33 96 0.84
34 10 0.09
35 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (31 bp):
ATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:30338 original size:66 final size:65
Alignment explanation
Indices: 30257--30387 Score: 192
Period size: 66 Copynumber: 2.0 Consensus size: 65
30247 ACGCGAAATT
* * * *
30257 AAATTCGTGTTGCGATTTTTATTTCGCATTGCG-ATTCCCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGAATT--CGCATTGCGATTTTCATTTCGCATTG
30321 CA
64 CA
30323 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGAAATTCGCATTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG-AATTCGCATTGCGATTTTCATTTCGCATTGC
30388 GATTCTCTCG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
66 56 0.95
68 3 0.05
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (65 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGAATTCGCATTGCGATTTTCATTTCGCATTGCA
Found at i:30354 original size:19 final size:19
Alignment explanation
Indices: 30266--30391 Score: 84
Period size: 19 Copynumber: 7.4 Consensus size: 19
30256 TAAATTCGTG
*
30266 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
30285 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
30299 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
30318 TTGC-A----AAATTCGCG
1 TTGCGATTTTCATTTCGCA
30332 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
30351 TTGCGA-----AATTCGCA
1 TTGCGATTTTCATTTCGCA
30365 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30384 TTGCGATT
1 TTGCGATT
30392 CTCTCGTTGC
Statistics
Matches: 79, Mismatches: 13, Indels: 30
0.65 0.11 0.25
Matches are distributed among these distances:
14 29 0.37
15 1 0.01
16 6 0.08
17 5 0.06
18 1 0.01
19 37 0.47
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:32271 original size:13 final size:12
Alignment explanation
Indices: 32242--32279 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
32232 TCTTCGGGGA
32242 CTTTTTCTTCTT
1 CTTTTTCTTCTT
32254 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
32266 GGTTTTTCTTCTT
1 -CTTTTTCTTCTT
32279 C
1 C
32280 AGGATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:33397 original size:20 final size:20
Alignment explanation
Indices: 33308--33399 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
33298 TGCGAATTTG
*
33308 GAAAATCGCAACGCGATACT
1 GAAAATCGCAACGAGATACT
** *
33328 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
33348 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
33369 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
33389 GAAAATCGCAA
1 GAAAATCGCAA
33400 TCATCTTCAA
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 40 0.73
21 15 0.27
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:33676 original size:20 final size:20
Alignment explanation
Indices: 33613--33680 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
33603 CAACGGGGAA
33613 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ***
33633 ATCACAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
33653 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
33673 ATCGCAAC
1 ATCGCAAC
33681 TAGAAAATCG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 5 0.15
20 24 0.71
21 5 0.15
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:33750 original size:19 final size:19
Alignment explanation
Indices: 33726--33774 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
33716 GATTATCTCG
33726 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
33745 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
33764 TTGTGATTTTC
1 TTGCGATTTTC
33775 TCGTTGCGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:35406 original size:42 final size:42
Alignment explanation
Indices: 35360--35452 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
35350 CCTCTTCAAC
* * *
35360 GATGACAGTGGCCTCTTGAACG-GTGGAGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGA-GGGGACTATTGAGA
* *
35402 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTATTGAGA
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTATTGAGA
*
35444 AATGACAGG
1 GATGACAGG
35453 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 39 0.91
43 4 0.09
ACGTcount: A:0.25, C:0.14, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTATTGAGA
Found at i:35432 original size:21 final size:20
Alignment explanation
Indices: 35350--35433 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 20
35340 GTGGGAGGTA
* * *
35350 CCTCTTCAACGATGACAGTGG
1 CCTCTTGAACGATG-GAGGGG
*
35371 CCTCTTGAACGGTGGAGGGGG
1 CCTCTTGAACGATGGA-GGGG
* ** *
35392 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATG-GAGGGG
35413 CCTCTTGAACGATTGGAGGGG
1 CCTCTTGAACGA-TGGAGGGG
35434 ACTATTGAGA
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
20 1 0.02
21 43 0.91
22 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.38, T:0.23
Consensus pattern (20 bp):
CCTCTTGAACGATGGAGGGG
Found at i:35840 original size:20 final size:20
Alignment explanation
Indices: 35817--35903 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
35807 AAACTTACTT
*
35817 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
35837 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
35857 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
35877 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
35896 TCGCAACG
1 TCGCAACG
35904 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 14 0.23
20 46 0.77
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:35841 original size:40 final size:40
Alignment explanation
Indices: 35797--35882 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
35787 TAGTTTACTT
* *
35797 TCGCAACAC-AAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGAAAA-TGACTATCGCAACGCGAAAATGACTA
* * * *
35837 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
35877 TCGCAA
1 TCGCAA
35883 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 36 0.92
41 3 0.08
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (40 bp):
TCGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
Found at i:36561 original size:18 final size:18
Alignment explanation
Indices: 36534--36580 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
36524 GGGTCGATCA
*
36534 GTGATGGCTCTAGGTGAG
1 GTGATGGCTCCAGGTGAG
* *
36552 GTGATAGCTCCGGGTGAG
1 GTGATGGCTCCAGGTGAG
36570 GTGATGGCTCC
1 GTGATGGCTCC
36581 CGAAATGGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.15, C:0.17, G:0.43, T:0.26
Consensus pattern (18 bp):
GTGATGGCTCCAGGTGAG
Found at i:37923 original size:20 final size:20
Alignment explanation
Indices: 37898--37935 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
37888 AATAGTTTCT
37898 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
37918 GAAAATGAAAATCGCAAC
1 GAAAATGAAAATCGCAAC
37936 GAGAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.18, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:38246 original size:22 final size:22
Alignment explanation
Indices: 38219--38262 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
38209 GATGGAGATA
38219 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
38241 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
38263 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:38926 original size:2 final size:2
Alignment explanation
Indices: 38915--38956 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
38905 AATCGGAAGA
38915 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38956 A
1 A
38957 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39373 original size:29 final size:27
Alignment explanation
Indices: 39315--39373 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
39305 AACATATTGG
* *
39315 AAATAAACATATAAAATTAATAAATGA
1 AAATAAACATATAAAAATAATAAATCA
39342 AAATAAAACTATATAAAAAATAAT-AATCA
1 AAAT-AAAC-ATAT-AAAAATAATAAATCA
39371 AAA
1 AAA
39374 CTAGTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 11 0.41
30 8 0.30
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (27 bp):
AAATAAACATATAAAAATAATAAATCA
Found at i:41704 original size:17 final size:17
Alignment explanation
Indices: 41682--41720 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
41672 AAATATACTT
41682 ATCTATTTAC-AGTTTAA
1 ATCTATTTACGA-TTTAA
41699 ATCTATTTACGATTTAA
1 ATCTATTTACGATTTAA
41716 ATCTA
1 ATCTA
41721 ATGGATTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (17 bp):
ATCTATTTACGATTTAA
Found at i:43388 original size:25 final size:24
Alignment explanation
Indices: 43346--43392 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
43336 TAATATATTA
*
43346 TATATAAAAAATATTTTCCAAAACC
1 TATATAAAAAATAATTT-CAAAACC
* *
43371 TATATAATATATAATTTCAAAA
1 TATATAAAAAATAATTTCAAAA
43393 TATTTTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (24 bp):
TATATAAAAAATAATTTCAAAACC
Found at i:43456 original size:29 final size:31
Alignment explanation
Indices: 43410--43477 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 31
43400 GAAATTGTAT
* *
43410 ATTATATACTTTTTAAAAATG-TTTT-CAAA
1 ATTATATACTTTTCAAAAATGTTTTTAAAAA
*
43439 ATTATATAGTTTTCAAAAATGTTTTTAAAAA
1 ATTATATACTTTTCAAAAATGTTTTTAAAAA
43470 ATTATATA
1 ATTATATA
43478 TTATATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 19 0.56
30 4 0.12
31 11 0.32
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (31 bp):
ATTATATACTTTTCAAAAATGTTTTTAAAAA
Found at i:43524 original size:29 final size:29
Alignment explanation
Indices: 43457--43531 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 29
43447 GTTTTCAAAA
* *
43457 ATGTTTTTAAAAAA--TTATATATTATAT
1 ATGTTTTTAAAAAATGTTTTATATAATAT
** *
43484 ATAATTTAAAAAAATGTTTTATATAATAT
1 ATGTTTTTAAAAAATGTTTTATATAATAT
43513 ATGTTTTT--AAAATGTTTTA
1 ATGTTTTTAAAAAATGTTTTA
43532 AAAACTATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
27 22 0.58
29 16 0.42
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (29 bp):
ATGTTTTTAAAAAATGTTTTATATAATAT
Found at i:43543 original size:36 final size:36
Alignment explanation
Indices: 43503--43756 Score: 206
Period size: 36 Copynumber: 7.1 Consensus size: 36
43493 AAAAATGTTT
*
43503 TATATAATATATGTTTTTAAAATGTTTTAAAAACTA
1 TATATAATATATGTTTTCAAAATGTTTTAAAAACTA
* **
43539 TATATTATATATACTTTCAAAATGTTTTAAAAA--A
1 TATATAATATATGTTTTCAAAATGTTTTAAAAACTA
* *
43573 TATATAATATA-----T--AAATGTTTTCAAAAATGTTT
1 TATATAATATATGTTTTCAAAATGTTTT-AAAAA--CTA
*
43605 TATATAATATATGTTTTTAAAATGTTTTAAAAACTA
1 TATATAATATATGTTTTCAAAATGTTTTAAAAACTA
* **
43641 TATATTATATATACTTTCAAAATGTTTTAAAAACTA
1 TATATAATATATGTTTTCAAAATGTTTTAAAAACTA
* * * *
43677 TATAATATATAAATGTTTTCAAAATATTTTTCAAAACCA
1 TAT-ATA-ATATATGTTTTCAAAAT-GTTTTAAAAACTA
* *
43716 TATACT-ATATA-GATTTTAAAAACGTTTTCAAAAACTA
1 TATA-TAATATATG-TTTTCAAAATGTTTT-AAAAACTA
43753 TATA
1 TATA
43757 ATATATACTT
Statistics
Matches: 175, Mismatches: 25, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
27 9 0.05
28 5 0.03
29 1 0.01
32 11 0.06
34 11 0.06
36 70 0.40
37 25 0.14
38 20 0.11
39 23 0.13
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATAATATATGTTTTCAAAATGTTTTAAAAACTA
Found at i:43609 original size:27 final size:27
Alignment explanation
Indices: 43558--43633 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
43548 TATACTTTCA
* * *
43558 AAATGTTTTAAAAAATATATAATAT-AT
1 AAATGTTTT-AAAAATGTTTTATATAAT
43585 AAATGTTTTCAAAAATGTTTTATATAAT
1 AAATGTTTT-AAAAATGTTTTATATAAT
* *
43613 ATATGTTTTTAAAATGTTTTA
1 AAATGTTTTAAAAATGTTTTA
43634 AAAACTATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 32 0.76
28 10 0.24
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (27 bp):
AAATGTTTTAAAAATGTTTTATATAAT
Found at i:43616 original size:102 final size:102
Alignment explanation
Indices: 43449--43700 Score: 418
Period size: 102 Copynumber: 2.5 Consensus size: 102
43439 ATTATATAGT
* **
43449 TTTCAAAAATGTTTTTAAAAAATTATATATTATATATAA--TTTAAAAAAATGTTTTATATAATA
1 TTTC-AAAATG-TTTTAAAAAA-TATATAATATATA-AATGTTTTCAAAAATGTTTTATATAATA
43512 TATGTTTTTAAAATGTTTTAAAAACTATATATTATATATAC
62 TATGTTTTTAAAATGTTTTAAAAACTATATATTATATATAC
43553 TTTCAAAATGTTTTAAAAAATATATAATATATAAATGTTTTCAAAAATGTTTTATATAATATATG
1 TTTCAAAATGTTTTAAAAAATATATAATATATAAATGTTTTCAAAAATGTTTTATATAATATATG
43618 TTTTTAAAATGTTTTAAAAACTATATATTATATATAC
66 TTTTTAAAATGTTTTAAAAACTATATATTATATATAC
*
43655 TTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAA
1 TTTCAAAATGTTTTAAAAAATATATAATATATAAATGTTTTCAAAA
43701 TATTTTTCAA
Statistics
Matches: 142, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
100 2 0.01
101 12 0.08
102 118 0.83
103 6 0.04
104 4 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (102 bp):
TTTCAAAATGTTTTAAAAAATATATAATATATAAATGTTTTCAAAAATGTTTTATATAATATATG
TTTTTAAAATGTTTTAAAAACTATATATTATATATAC
Found at i:43642 original size:27 final size:28
Alignment explanation
Indices: 43587--43643 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
43577 TAATATATAA
*
43587 ATGTTTTCAAAAATGTTTTATATAATAT
1 ATGTTTTCAAAAATGTTTTATAAAATAT
*
43615 ATGTTTT-TAAAATGTTTTA-AAAACTAT
1 ATGTTTTCAAAAATGTTTTATAAAA-TAT
43642 AT
1 AT
43644 ATTATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 3 0.12
27 16 0.62
28 7 0.27
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (28 bp):
ATGTTTTCAAAAATGTTTTATAAAATAT
Found at i:43772 original size:76 final size:77
Alignment explanation
Indices: 43629--43786 Score: 203
Period size: 75 Copynumber: 2.1 Consensus size: 77
43619 TTTTAAAATG
* * * * * * *
43629 TTTTAAAAACTATATATTATATATACTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTT
1 TTTTCAAAACCATATACTATATAGACTTTAAAAACGTTTTAAAAACTATATAATATATAAATATT
43694 TTC-AAAAT-AT
66 TTCGAAAATCAT
* **
43704 TTTTCAAAACCATATACTATATAGATTTTAAAAACGTTTTCAAAAACTATATAATATATACTTAT
1 TTTTCAAAACCATATACTATATAGACTTTAAAAACGTTTT-AAAAACTATATAATATATAAATAT
43769 TTTCGAAAATCAT
65 TTTCGAAAATCAT
43782 TTTTC
1 TTTTC
43787 CGAAAATTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
75 33 0.47
76 25 0.36
77 5 0.07
78 7 0.10
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (77 bp):
TTTTCAAAACCATATACTATATAGACTTTAAAAACGTTTTAAAAACTATATAATATATAAATATT
TTCGAAAATCAT
Found at i:43808 original size:76 final size:75
Alignment explanation
Indices: 43629--43827 Score: 199
Period size: 75 Copynumber: 2.6 Consensus size: 75
43619 TTTTAAAATG
* * * * *
43629 TTTTAAAAACTATATATTATATATACTTTCAAAATGTTTT-AAAAACTATATAATATATAAATGT
1 TTTTCAAAAC-ATATACTATATATATTTTCAAAACGTTTTCAAAAACTATATAATATATAAATAT
43693 TTTCAAAATAT
65 TTTCAAAATAT
* * **
43704 TTTTCAAAACCATATACTATATAGATTTTAAAAACGTTTTCAAAAACTATATAATATATACTTAT
1 TTTTCAAAA-CATATACTATATATATTTTCAAAACGTTTTCAAAAACTATATAATATATAAATAT
43769 TTTCGAAAATCAT
65 TTTC-AAAAT-AT
* *
43782 TTTTCCGAAAA-TTATAC-AT-TATATTTTGTCAAAACATTTTCAAAAA
1 TTTT-C-AAAACATATACTATATATA-TTT-TCAAAACGTTTTCAAAAA
43828 TTGTATTACT
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
75 32 0.31
76 29 0.28
77 10 0.10
78 27 0.26
79 1 0.01
80 4 0.04
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (75 bp):
TTTTCAAAACATATACTATATATATTTTCAAAACGTTTTCAAAAACTATATAATATATAAATATT
TTCAAAATAT
Found at i:46777 original size:142 final size:142
Alignment explanation
Indices: 46521--46781 Score: 355
Period size: 142 Copynumber: 1.8 Consensus size: 142
46511 GAGGTATGGC
* ** ** * * *
46521 TTAAACTTTTATCATTTGAATGTCAGCTACCTACTGTACCTATGTGAGTGGCATGCCATGCGACT
1 TTAAACGTTTATCATTCAAATACCAGATACCTACTGTACATACGTGAGTGGCATGCCATGCGACT
* * * *
46586 TTTCCAGCTACGCGAGAGGACCCCGAGGAGATGCATTCAGCCACTTGCAACCCAGCCCCCCTTGA
66 TTTCCAGCCACACGAGAGGACCCCGAGGAGACGCATGCAGCCACTTGCAACCCAGCCCCCCTTGA
46651 GAGACACATAGG
131 GAGACACATAGG
*
46663 TTAAACGTTTATCATTCAAATACCAGATACCTATTGTACATACGTGAGTGGCATGCCATGCGACT
1 TTAAACGTTTATCATTCAAATACCAGATACCTACTGTACATACGTGAGTGGCATGCCATGCGACT
* *
46728 TTGT-CAGCCACACGAGGGGACCCTGAGGAGACGCATGC-GACCACTTGCAACCCA
66 TT-TCCAGCCACACGAGAGGACCCCGAGGAGACGCATGCAG-CCACTTGCAACCCA
46782 AACCGCCCCT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
141 1 0.01
142 100 0.98
143 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (142 bp):
TTAAACGTTTATCATTCAAATACCAGATACCTACTGTACATACGTGAGTGGCATGCCATGCGACT
TTTCCAGCCACACGAGAGGACCCCGAGGAGACGCATGCAGCCACTTGCAACCCAGCCCCCCTTGA
GAGACACATAGG
Found at i:71119 original size:30 final size:27
Alignment explanation
Indices: 71083--71144 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
71073 GAAAAAATTT
*
71083 AATAAAATAAAATAGATAATAATAATAATA
1 AATAAAAGAAAA-A-ATAATAA-AATAATA
**
71113 AATAAAAGGGAAAATAATAAAATAATA
1 AATAAAAGAAAAAATAATAAAATAATA
71140 AATAA
1 AATAA
71145 TAGTAGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 12 0.41
28 7 0.24
29 1 0.03
30 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (27 bp):
AATAAAAGAAAAAATAATAAAATAATA
Found at i:71698 original size:12 final size:12
Alignment explanation
Indices: 71683--71712 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
71673 AAAAGTACAC
71683 GAAAAATAGAGA
1 GAAAAATAGAGA
*
71695 GAAAACTAGAGA
1 GAAAAATAGAGA
71707 GAAAAA
1 GAAAAA
71713 GAAAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:73828 original size:22 final size:22
Alignment explanation
Indices: 73811--73877 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
73801 CTCGTATAAA
73811 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
73833 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
73855 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
73877 T
1 T
73878 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:74145 original size:30 final size:31
Alignment explanation
Indices: 74095--74154 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
74085 TAGACATAGT
*
74095 ATTTCCATAACTTTAACACATAG-GCATATC
1 ATTTACATAACTTTAACACATAGTGCATATC
* *
74125 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATAACTTTAACACATAGTGCATAT
74155 AACTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATAACTTTAACACATAGTGCATATC
Found at i:74668 original size:21 final size:21
Alignment explanation
Indices: 74638--74680 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
74628 ATTCATTTCG
* *
74638 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
74659 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
74680 T
1 T
74681 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:74680 original size:67 final size:67
Alignment explanation
Indices: 74510--74658 Score: 219
Period size: 67 Copynumber: 2.2 Consensus size: 67
74500 CTTTTCTCAT
* *
74510 GGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
*
74575 AG
66 AA
** * * *
74577 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
74641 AA
66 AA
74643 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
74659 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
66 22 0.30
67 52 0.70
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AA
Found at i:80732 original size:22 final size:22
Alignment explanation
Indices: 80715--80781 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
80705 CTCGTATAAA
80715 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
80737 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
80759 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
80781 T
1 T
80782 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:81051 original size:30 final size:31
Alignment explanation
Indices: 81001--81060 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
80991 TAGACATAGT
*
81001 ATTTCCATAACTTTAACACATAG-GCATATC
1 ATTTACATAACTTTAACACATAGTGCATATC
* *
81031 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATAACTTTAACACATAGTGCATAT
81061 AACTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATAACTTTAACACATAGTGCATATC
Found at i:81538 original size:71 final size:67
Alignment explanation
Indices: 81417--81571 Score: 211
Period size: 71 Copynumber: 2.3 Consensus size: 67
81407 TTTTTCTCAT
* *
81417 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACG-
81482 TGATGA
64 T--TGA
** * *
81488 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGTT
81553 GA
66 GA
*
81555 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
81572 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
67 19 0.25
69 1 0.01
70 3 0.04
71 54 0.70
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGTT
GA
Found at i:81581 original size:21 final size:21
Alignment explanation
Indices: 81551--81593 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
81541 ATTCATTTCG
* *
81551 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
81572 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
81593 T
1 T
81594 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:82763 original size:32 final size:32
Alignment explanation
Indices: 82722--82838 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
82712 AGAGCATCGC
*
82722 ATTCAGATAATGCACAACAGTGTTAGTGTTGA
1 ATTCAGATAATGCACAACAGTGTCAGTGTTGA
* * * * *
82754 ATTCAGATAATGTATAGCAGTGTCAGTGTCGT
1 ATTCAGATAATGCACAACAGTGTCAGTGTTGA
* *
82786 ATTAAGATAATGCACAACAGTGTCAGTG-TCA
1 ATTCAGATAATGCACAACAGTGTCAGTGTTGA
*
82817 CATTCAAATAATGCACAACAGT
1 -ATTCAGATAATGCACAACAGT
82839 ACGTGTCATG
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (32 bp):
ATTCAGATAATGCACAACAGTGTCAGTGTTGA
Found at i:82867 original size:36 final size:36
Alignment explanation
Indices: 82805--82873 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
82795 ATGCACAACA
*
82805 GTGTCAGTGTCACATTCAAATAATGCACAACAGTAC
1 GTGTCAGTGACACATTCAAATAATGCACAACAGTAC
* *
82841 GTGTCATGTGACACATTTAAGT-ATGCACAACAG
1 GTGTCA-GTGACACATTCAAATAATGCACAACAG
82874 CTACAATCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 17 0.59
37 12 0.41
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (36 bp):
GTGTCAGTGACACATTCAAATAATGCACAACAGTAC
Found at i:84538 original size:183 final size:184
Alignment explanation
Indices: 84229--84615 Score: 647
Period size: 183 Copynumber: 2.1 Consensus size: 184
84219 TTTTCTAATT
* * * *
84229 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
*
84293 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
*
84358 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
84412 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAA
* *
84476 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTGAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
84540 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
*
84595 TATATAATATAGTTAATATTT
1 TATATAATATATTTAATATTT
84616 AAAATTTAAT
Statistics
Matches: 192, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
182 2 0.01
183 125 0.65
184 65 0.34
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:88126 original size:60 final size:60
Alignment explanation
Indices: 87999--88126 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
87989 AAATGGTCCT
* * *
87999 CCGACTATATGACATTGCTTTGTTGAGTATCTCAACTATTAAAAGTTATAAAATAGTCTC
1 CCGACTATAGGACATTGCTTTGTTGAGTACCTCAACTATTAAAAGTTATAAAATAGGCTC
*** ** * *
88059 TTAACTATAGGATGTTGCTTTGTTGAGTCCCTTGAA-TATTAAAAGTTATAAAAT-GGCTAC
1 CCGACTATAGGACATTGCTTTGTTGAGTACC-TCAACTATTAAAAGTTATAAAATAGGCT-C
88119 CCGACTAT
1 CCGACTAT
88127 TCATTATATT
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
59 3 0.06
60 47 0.89
61 3 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (60 bp):
CCGACTATAGGACATTGCTTTGTTGAGTACCTCAACTATTAAAAGTTATAAAATAGGCTC
Found at i:92125 original size:13 final size:13
Alignment explanation
Indices: 92107--92137 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
92097 ATTAAAATCT
92107 TTAAATCCAAACA
1 TTAAATCCAAACA
*
92120 TTAAATCCAATCA
1 TTAAATCCAAACA
92133 TTAAA
1 TTAAA
92138 ATTATACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAAATCCAAACA
Found at i:94638 original size:18 final size:19
Alignment explanation
Indices: 94598--94638 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
94588 TTTTTATTTA
*
94598 TTTATAATTTATACTAATT
1 TTTATAATTTATACTAATG
*
94617 TTTATAATTTA-ATTAATG
1 TTTATAATTTATACTAATG
94635 TTTA
1 TTTA
94639 CAGTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATAATTTATACTAATG
Found at i:96509 original size:17 final size:16
Alignment explanation
Indices: 96489--96531 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
96479 TAATTATATG
*
96489 AATTAAACAAATGACTA
1 AATTAAACAAAT-ACAA
*
96506 AATTGAAATAAATACAA
1 AATT-AAACAAATACAA
96523 AATTAAACA
1 AATTAAACA
96532 TGCAATTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 7 0.32
ACGTcount: A:0.63, C:0.09, G:0.05, T:0.23
Consensus pattern (16 bp):
AATTAAACAAATACAA
Found at i:96857 original size:5 final size:5
Alignment explanation
Indices: 96850--96903 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
96840 TCCCTTCTCT
* * * *
96850 CTTCT CTTCT CTTCT CTTCT CTTCA CTTCA CTTCA CTTCA CTTCA CTTCA
1 CTTCA CTTCA CTTCA CTTCA CTTCA CTTCA CTTCA CTTCA CTTCA CTTCA
96900 CTTC
1 CTTC
96904 TCTACCCTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.11, C:0.41, G:0.00, T:0.48
Consensus pattern (5 bp):
CTTCA
Found at i:97637 original size:15 final size:15
Alignment explanation
Indices: 97617--97657 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
97607 CGGGTACGCG
*
97617 TCCACCCGTCCCGCA
1 TCCACCCGCCCCGCA
97632 TCCACCCGCCCCGCA
1 TCCACCCGCCCCGCA
*
97647 TCCGCCCGCCC
1 TCCACCCGCCC
97658 AACTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.66, G:0.15, T:0.10
Consensus pattern (15 bp):
TCCACCCGCCCCGCA
Found at i:97881 original size:7 final size:7
Alignment explanation
Indices: 97869--97899 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
97859 TTCTTCTTCT
97869 TCTTTAA
1 TCTTTAA
97876 TCTTTAA
1 TCTTTAA
97883 TCTTTAA
1 TCTTTAA
97890 TCTTTAA
1 TCTTTAA
97897 TCT
1 TCT
97900 CTGTGCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTTTAA
Found at i:98533 original size:2 final size:2
Alignment explanation
Indices: 98526--98555 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
98516 AGTGTGCTTA
98526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98556 TATTCTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102918 original size:90 final size:90
Alignment explanation
Indices: 102808--102999 Score: 323
Period size: 90 Copynumber: 2.1 Consensus size: 90
102798 TATCGGTACC
* * *
102808 CCTTTGGGTATCGGTACCATTTTTGCATTCTGGAATTTGAGCAATACTGGTAGTATCGATACTAC
1 CCTTTGGATATCGATACCATTTTTACATTCTGGAATTTGAGCAATACTGGTAGTATCGATACTAC
*
102873 CTAGTGAGTATCGATACTTCCCTTA
66 CTAGTGAATATCGATACTTCCCTTA
* *
102898 CCTTTGGATATTGATACCATTTTTACATTCTGGAATTTGAGCAATGCTGGTAGTATCGATACTAC
1 CCTTTGGATATCGATACCATTTTTACATTCTGGAATTTGAGCAATACTGGTAGTATCGATACTAC
102963 CTAGTGAATATCGATACTTCCCTTA
66 CTAGTGAATATCGATACTTCCCTTA
102988 CCTTTGG-TATCG
1 CCTTTGGATATCG
103000 GTACTATTCA
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 4 0.04
90 91 0.96
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (90 bp):
CCTTTGGATATCGATACCATTTTTACATTCTGGAATTTGAGCAATACTGGTAGTATCGATACTAC
CTAGTGAATATCGATACTTCCCTTA
Found at i:109294 original size:23 final size:22
Alignment explanation
Indices: 109234--109311 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
109224 AAATCAAATC
109234 AAAAAAATAA-ATAAATAATAAA
1 AAAAAAATAATA-AAATAATAAA
* *
109256 AAAAAAATATTAAAATATTAAA
1 AAAAAAATAATAAAATAATAAA
* *
109278 AAAACAAA-AAT-AGA-AATAGA
1 AAAA-AAATAATAAAATAATAAA
*
109298 AATAAAATAATAAA
1 AAAAAAATAATAAA
109312 TCAAAGGGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
19 3 0.07
20 10 0.23
21 3 0.07
22 24 0.55
23 4 0.09
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (22 bp):
AAAAAAATAATAAAATAATAAA
Found at i:112900 original size:23 final size:21
Alignment explanation
Indices: 112873--112915 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
112863 ACTGTTAAAA
112873 AATCTTTATCCTCTTAAAAAATT
1 AATC-TTAT-CTCTTAAAAAATT
*
112896 AATCTTATCTTTTAAAAAAT
1 AATCTTATCTCTTAAAAAAT
112916 ATTTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 4 0.21
23 4 0.21
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (21 bp):
AATCTTATCTCTTAAAAAATT
Found at i:112922 original size:19 final size:20
Alignment explanation
Indices: 112867--112922 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
112857 GAAATCACTG
*
112867 TTAAAAAAT-CTTTATCCTC
1 TTAAAAAATATTTTATCCTC
* *
112886 TTAAAAAATTAATCTTAT-CTT
1 TTAAAAAA-T-ATTTTATCCTC
112907 TTAAAAAATATTTTAT
1 TTAAAAAATATTTTAT
112923 AAAATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 14 0.47
20 2 0.07
21 10 0.33
22 4 0.13
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAAAATATTTTATCCTC
Found at i:116131 original size:14 final size:14
Alignment explanation
Indices: 116112--116139 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
116102 TGTTATGGCC
116112 TTATAAATTACTAA
1 TTATAAATTACTAA
116126 TTATAAATTACTAA
1 TTATAAATTACTAA
116140 ACAACATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATAAATTACTAA
Found at i:120165 original size:7 final size:7
Alignment explanation
Indices: 120153--120180 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
120143 TTTCTTATAT
120153 TAATTAA
1 TAATTAA
120160 TAATTAA
1 TAATTAA
120167 TAATTAA
1 TAATTAA
120174 TAATTAA
1 TAATTAA
120181 AAATACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATTAA
Found at i:121764 original size:12 final size:12
Alignment explanation
Indices: 121734--121758 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
121724 TACCCATTTT
121734 ATATTTAATTGA
1 ATATTTAATTGA
121746 ATATTTAATTGA
1 ATATTTAATTGA
121758 A
1 A
121759 AGTTTATCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATTTAATTGA
Found at i:122541 original size:158 final size:159
Alignment explanation
Indices: 122231--122599 Score: 446
Period size: 158 Copynumber: 2.4 Consensus size: 159
122221 AATGATTTCA
* * * * * *
122231 TTATTTCTTCAATTCCTCCTTCATTTTAAGT-TCATTTTTTACCAAATTTGAACTACATGCTCCT
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCTCATTTTTTACAAAATTTGAACCACAAGCTCCT
* * *
122295 AAACCATAGTAGGATACATGTGTACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTTA
66 AAACCATAGTAGAATACATGTATACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCA
** *
122360 ATTTAGTCCTTCAATTTTTCATAATCTCC
131 ATTTAGTCCTTCAAAGTTTCATAATATCC
* ** * *
122389 TTATTTCTTCAATTCGTTATTTATTTTAAGTCTGTTTTTTTACAAAATTTGAGCCACAAGCTTCT
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCTCATTTTTTACAAAATTTGAACCACAAGCTCCT
* * *
122454 AAACCATAGTATAATACATGTATACTTTCAATTCCTTTTTTTGATAACAAA-TTTTTATTTTTCA
66 AAACCATAGTAGAATACATGTATACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCA
* *
122518 ATTTAGTTCTTCAAAGTTTCATAATATTC
131 ATTTAGTCCTTCAAAGTTTCATAATATCC
* * * * *
122547 TTATTCCATCAATTTGTGATTTATTTT-AGTCTC----TTTACCAAATTTGAACCACA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCTCATTTTTTACAAAATTTGAACCACA
122600 TGCCATATAC
Statistics
Matches: 181, Mismatches: 29, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
153 18 0.10
157 5 0.03
158 86 0.48
159 72 0.40
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (159 bp):
TTATTTCTTCAATTCGTCATTTATTTTAAGTCTCATTTTTTACAAAATTTGAACCACAAGCTCCT
AAACCATAGTAGAATACATGTATACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCA
ATTTAGTCCTTCAAAGTTTCATAATATCC
Found at i:123765 original size:64 final size:64
Alignment explanation
Indices: 123681--123818 Score: 199
Period size: 64 Copynumber: 2.2 Consensus size: 64
123671 ACTAAGGGTG
* * *
123681 ATCGATGCATAAAATACATTCGATGTTTTAA-ACAAGCCTGGAGTGCATCGATGCATGGTCTGTG
1 ATCGATGCATAAAATACATTCAATGTTTCAATAAAAGCCT-GAGTGCATCGATGCATGG-CTGTG
123745 C
64 C
* *
123746 ATCGATGCAT-AAATGCATTCAATGTTTCAATAAAATCCTGAGTGCATCGATGCATGGCTGTGC
1 ATCGATGCATAAAATACATTCAATGTTTCAATAAAAGCCTGAGTGCATCGATGCATGGCTGTGC
123809 ATCGATGCAT
1 ATCGATGCAT
123819 CCCTTCACAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
63 16 0.24
64 35 0.52
65 16 0.24
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (64 bp):
ATCGATGCATAAAATACATTCAATGTTTCAATAAAAGCCTGAGTGCATCGATGCATGGCTGTGC
Found at i:124416 original size:2 final size:2
Alignment explanation
Indices: 124409--124483 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
124399 AACCAACCAA
124409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124450 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
124484 ATAAGTTCAA
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:125343 original size:291 final size:292
Alignment explanation
Indices: 124766--125348 Score: 1007
Period size: 291 Copynumber: 2.0 Consensus size: 292
124756 ATGGGAGGCA
124766 ATTTGTTCCTCTTGTTGTGTTGGCCATCGTCTGGTACGTGATCGTCAATATCTTGCATAACTGTT
1 ATTTGTTCCTCTTGTTGTGTTGGCCATCGTCTGGTACGTGATCGTCAATATCTTGCATAACTGTT
*
124831 GAAACTCTGGATCATTGTCCGCAGCTGGTACCGGTTATAGGTGGAGCACAAGAAGTGCTAGGTGC
66 GAAACTCTGGATCATTGTCCGCAGCTGGTACCGG-T-TAGGTAGAGCACAAGAAGTGCTAGGTGC
*
124896 AGGAGGAGCTCGTGAGGAACTAGCGCCCGGTGTTTGCTCAGTGGGTCTATATTCCCATTGACACC
129 AGGAGGAGCTCGTGAGGAACTAGCGCCCAGTGTTTGCTCAGTGGGTCTATATTCCCATTGACACC
124961 GTTACCTTATCTTGTTTCTATCCGGCTTTCTTTAAGGAAGTTAGGTTGATTTGGTTTAGAGAGGC
194 GTTACCTTATCTTGTTTCTATCCGGCTTTCTTTAAGGAAGTTAGGTTGATTTGGTTTAGAGAGGC
125026 ATGGGATGTCAACCGAGACCTAAGTTGTAGTCGC
259 ATGGGATGTCAACCGAGACCTAAGTTGTAGTCGC
125060 ATTTGTTCCTCTTG-TGTG-TGGCTCATCGTCTGGTACGTGATCGTCAATATCTTGCATAAGCTG
1 ATTTGTTCCTCTTGTTGTGTTGGC-CATCGTCTGGTACGTGATCGTCAATATCTTGCATAA-CTG
* * *
125123 TTGAAACTCTGGATCATTGTCCGTAGCTGGTACCGG-TAGGTATAGCATAAGAAGTGCTAGGTGC
64 TTGAAACTCTGGATCATTGTCCGCAGCTGGTACCGGTTAGGTAGAGCACAAGAAGTGCTAGGTGC
125187 AGGAGGAGCTCGTGAGGAACTAGCGCCCAGTGTTTGCTCAGTGGGTCTATATTCCCATTGAC-CC
129 AGGAGGAGCTCGTGAGGAACTAGCGCCCAGTGTTTGCTCAGTGGGTCTATATTCCCATTGACACC
*
125251 -TTACCTTATCTTG-TTCTATCCGGCTTTCTTTAAGGAAGTTAGGTTGATTTGGTTTTGGAGAGG
194 GTTACCTTATCTTGTTTCTATCCGGCTTTCTTTAAGGAAGTTAGGTTGATTTGG-TTTAGAGAGG
125314 CATGGGAATGTCAACCGAGACCTTAAGTTGTAGTC
258 CATGGG-ATGTCAACCGAGACC-TAAGTTGTAGTC
125349 AGATAAATAG
Statistics
Matches: 278, Mismatches: 6, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
288 39 0.14
289 28 0.10
290 17 0.06
291 98 0.35
292 4 0.01
293 40 0.14
294 52 0.19
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (292 bp):
ATTTGTTCCTCTTGTTGTGTTGGCCATCGTCTGGTACGTGATCGTCAATATCTTGCATAACTGTT
GAAACTCTGGATCATTGTCCGCAGCTGGTACCGGTTAGGTAGAGCACAAGAAGTGCTAGGTGCAG
GAGGAGCTCGTGAGGAACTAGCGCCCAGTGTTTGCTCAGTGGGTCTATATTCCCATTGACACCGT
TACCTTATCTTGTTTCTATCCGGCTTTCTTTAAGGAAGTTAGGTTGATTTGGTTTAGAGAGGCAT
GGGATGTCAACCGAGACCTAAGTTGTAGTCGC
Found at i:126264 original size:13 final size:13
Alignment explanation
Indices: 126246--126270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
126236 TTAAAATTAT
126246 TTTGAAAATAATG
1 TTTGAAAATAATG
126259 TTTGAAAATAAT
1 TTTGAAAATAAT
126271 ATATATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
TTTGAAAATAATG
Found at i:126276 original size:2 final size:2
Alignment explanation
Indices: 126269--126320 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
126259 TTTGAAAATA
126269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
126311 AT AT AT AT AT
1 AT AT AT AT AT
126321 TCATGAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126806 original size:23 final size:23
Alignment explanation
Indices: 126780--126885 Score: 110
Period size: 23 Copynumber: 4.7 Consensus size: 23
126770 ATGAACTGCT
*
126780 GAGTGCATTGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
126803 GAGTGCATCGGTGCACCTTCAAG
1 GAGTGCATCGATGCACATTCAAG
* * *
126826 GAGTGCATCGGTGCACCTTC-AT
1 GAGTGCATCGATGCACATTCAAG
* *
126848 G-GTGTATCGATGCATATTCAAAG
1 GAGTGCATCGATGCACATTC-AAG
126871 GA-TGCATCGATGCAC
1 GAGTGCATCGATGCAC
126886 TGACGAGTGT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
21 14 0.20
22 2 0.03
23 53 0.77
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:128008 original size:30 final size:30
Alignment explanation
Indices: 127991--128080 Score: 180
Period size: 30 Copynumber: 3.0 Consensus size: 30
127981 TCCGAAGAAC
127991 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
128021 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
128051 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
128081 TTGTCCATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:128120 original size:31 final size:31
Alignment explanation
Indices: 128082--128175 Score: 118
Period size: 31 Copynumber: 3.0 Consensus size: 31
128072 CCTCGGTAAT
* *
128082 TGTCCATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATATGTTCCATAGAACATAGGTAAAC
* *
128113 TGTCCATATGTCTCGAAAG-ACATAGGTAAAAC
1 TGTCCATATGT-TCCATAGAACATAGGT-AAAC
*
128145 TGTCCATATGTTCCGTAGAACATAGGTAAAC
1 TGTCCATATGTTCCATAGAACATAGGTAAAC
128176 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 27 0.51
32 26 0.49
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (31 bp):
TGTCCATATGTTCCATAGAACATAGGTAAAC
Found at i:128168 original size:32 final size:32
Alignment explanation
Indices: 128082--128174 Score: 120
Period size: 32 Copynumber: 2.9 Consensus size: 32
128072 CCTCGGTAAT
* *
128082 TGTCCATATGTTCCTTAGAACATAGGT-ATAC
1 TGTCCATATGTTCCGTAGAACATAGGTAAAAC
*
128113 TGTCCATATG-TCTCG-AAAGACATAGGTAAAAC
1 TGTCCATATGTTC-CGTAGA-ACATAGGTAAAAC
128145 TGTCCATATGTTCCGTAGAACATAGGTAAA
1 TGTCCATATGTTCCGTAGAACATAGGTAAA
128175 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
30 4 0.08
31 19 0.36
32 26 0.49
33 4 0.08
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
TGTCCATATGTTCCGTAGAACATAGGTAAAAC
Found at i:129070 original size:21 final size:20
Alignment explanation
Indices: 129040--129083 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
129030 ATTTTGTTCG
* *
129040 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
129060 TTGAATGGGTACCGATTCCCC
1 TTGAA-GGGTACCGATTCCCC
129081 TTG
1 TTG
129084 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:131878 original size:30 final size:30
Alignment explanation
Indices: 131844--131940 Score: 176
Period size: 30 Copynumber: 3.2 Consensus size: 30
131834 CTCGAAGAAC
131844 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
131874 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
131904 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
131934 CTGTCCA
1 CTATCCA
131941 TATGTTCCTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:131971 original size:31 final size:30
Alignment explanation
Indices: 131929--132026 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
131919 AAAGATCCTC
*
131929 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
131959 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
* * *
131990 GGTAAAACTGTTCATATGTTCCGTAGAAAATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
132022 GGTAA
1 GGTAA
132027 ACCATCTAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.45
32 23 0.42
33 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:132023 original size:32 final size:32
Alignment explanation
Indices: 131932--132027 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 32
131922 GATCCTCGGT
* *
131932 AACTGTCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAAAATAGGTAA
*
131963 TACTGTCCATATG-TCTCG-A-AAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGAA-A-ATAGGTAA
*
131995 AACTGTTCATATGTTCCGTAGAAAATAGGTAA
1 AACTGTCCATATGTTCCGTAGAAAATAGGTAA
132027 A
1 A
132028 CCATCTAGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
29 2 0.04
30 3 0.06
31 19 0.36
32 23 0.43
33 4 0.08
34 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAAAATAGGTAA
Found at i:132539 original size:19 final size:19
Alignment explanation
Indices: 132502--132540 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
132492 TGAGGCAATC
*
132502 ATTAGATACCTACACCTTA
1 ATTAGATACCTACAACTTA
132521 ATTAGATA-CTAGCAACTTA
1 ATTAGATACCTA-CAACTTA
132540 A
1 A
132541 ACGAACTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (19 bp):
ATTAGATACCTACAACTTA
Found at i:139965 original size:46 final size:46
Alignment explanation
Indices: 139893--139994 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
139883 CTAAGGGTGA
* * *
139893 ATCGATGTATAAAATACATTCAATGTTTTAA-ACAAGCCTGGAATGC
1 ATCGATGCATAAAATACATTCAATGTTTCAATAAAAGCCT-GAATGC
* * * *
139939 ATCGATGCATAAAATGCATTCGATGTTTCAATAAAATCCTGAGTGC
1 ATCGATGCATAAAATACATTCAATGTTTCAATAAAAGCCTGAATGC
139985 ATCGATGCAT
1 ATCGATGCAT
139995 GGCTGTGCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 42 0.88
47 6 0.12
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (46 bp):
ATCGATGCATAAAATACATTCAATGTTTCAATAAAAGCCTGAATGC
Found at i:140939 original size:2 final size:2
Alignment explanation
Indices: 140932--140966 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
140922 TGAAAGAATA
140932 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
140967 TATGTATGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:141122 original size:2 final size:2
Alignment explanation
Indices: 141115--141144 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
141105 AAAAATATCA
*
141115 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
141145 GGTTAGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:141277 original size:173 final size:170
Alignment explanation
Indices: 140946--141288 Score: 634
Period size: 173 Copynumber: 2.0 Consensus size: 170
140936 ATATATATAT
*
140946 TATATATATATATATATATATTATGTATGGTTAGATAAAATCAAAAAATTAGAATAAATATTTTC
1 TATATATATATATATATATATTATATATGGTTAGATAAAATCAAAAAATTAGAATAAATATTTTC
141011 ATAATAATATAAATAATTAAACAAAATTAGTATAGAACTTGAATAATTTGATTTAAATAACTTTA
66 ATAATAATATAAATAATTAAACAAAATTAGTATAGAACTTGAATAATTTGATTTAAATAACTTTA
141076 CTCAAATTTCTTAAACTTGAATCGACTCGAAAAATATCAA
131 CTCAAATTTCTTAAACTTGAATCGACTCGAAAAATATCAA
141116 TATATATATATATATATATATGTATATATGGTTAGATAAAATCAAAAAATTAGAATAAAATATTT
1 TATATATATATATATATATAT-TATATATGGTTAGATAAAATCAAAAAATTAGAAT-AAATATTT
141181 TCATAATAATAT-AATAATTATAACAAAATTAGTATAGAAACTTGAATAATTTGATTTAAATAAC
64 TCATAATAATATAAATAATTA-AACAAAATTAGTATAG-AACTTGAATAATTTGATTTAAATAAC
141245 TTTACTCAAATTTCTTAAACTTGAATCGACTCGAAAAATATCAA
127 TTTACTCAAATTTCTTAAACTTGAATCGACTCGAAAAATATCAA
141289 GTTAAGTTCG
Statistics
Matches: 168, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
170 21 0.12
171 41 0.24
172 36 0.21
173 70 0.42
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (170 bp):
TATATATATATATATATATATTATATATGGTTAGATAAAATCAAAAAATTAGAATAAATATTTTC
ATAATAATATAAATAATTAAACAAAATTAGTATAGAACTTGAATAATTTGATTTAAATAACTTTA
CTCAAATTTCTTAAACTTGAATCGACTCGAAAAATATCAA
Found at i:145186 original size:306 final size:307
Alignment explanation
Indices: 144809--145421 Score: 1171
Period size: 306 Copynumber: 2.0 Consensus size: 307
144799 CGCATAGTAT
144809 CATCATCAAAAACCATAAATCAAACCAAATGCTACTCTTCTTTACCCCCAATAAATTTCCAGCAA
1 CATCATCAAAAACCATAAATCAAACCAAATGCTACTCTTCTTTACCCCCAATAAATTTCCAGCAA
144874 TAAAGTTGGAAATAAAAGTATGTATATGTTATGGGATAAAACTATGGCAATGCTTTTGCATTCAC
66 TAAAGTTGGAAAT-AAAGTATGTATATG-TATGGGATAAAACTATGGCAATGCTTTTGCATTCAC
144939 ATTTTATTTGAATTCTCCAGCTTCCTTTGTCACCCTCTGGGAAAATGAGATGGGAA-CAAGCAAA
129 ATTTTATTTGAATTCTCCAGCTTCCTTTGTCACCCTCTGGGAAAATGAGATGGGAACCAAGCAAA
145003 GTCCTCTACTTCTTAGATC-TGTTGCTTCCTTCCGATTTCCTGCTAAATAAATGCAATTTTATAA
194 GTCCTCTACTTCTTAGATCTTGTTGCTTCCTTCCGATTTCCTGCTAAATAAATGCAATTTTATAA
145067 AATAAGATTTAAATTATACATTGTTACAATGAGGAAT-AAAACCCAAAA
259 AATAAGATTTAAATTATACATTGTTACAATGAGGAATAAAAACCCAAAA
145115 CATCATCAAAAACCATAAATCAAACCAAATGCTACTCTTCTTTACCCCCAATAAATTT-CAGCAA
1 CATCATCAAAAACCATAAATCAAACCAAATGCTACTCTTCTTTACCCCCAATAAATTTCCAGCAA
145179 TTAAAGTTGGAAATAAAGTATGTATATGTATGGGATAAAACTATGGCAATGCTTTTGCATTCACA
66 -TAAAGTTGGAAATAAAGTATGTATATGTATGGGATAAAACTATGGCAATGCTTTTGCATTCACA
145244 TTTTATTTGAATTCTCCAGCTTCCTTTGTCACCCTCTGGGAAAATGAGATGGGAACCAAGCAAAG
130 TTTTATTTGAATTCTCCAGCTTCCTTTGTCACCCTCTGGGAAAATGAGATGGGAACCAAGCAAAG
145309 TCCTCTACTTCTTAGATCTTGTTGCTTCCTTCCGATTTCCTGCTAAATAAATGCAATTTTATAAA
195 TCCTCTACTTCTTAGATCTTGTTGCTTCCTTCCGATTTCCTGCTAAATAAATGCAATTTTATAAA
145374 ATAAGATTTAAATTATACATTGTTACAATGAGGAATAAAAACCCAAAA
260 ATAAGATTTAAATTATACATTGTTACAATGAGGAATAAAAACCCAAAA
145422 AGAAAATTTC
Statistics
Matches: 303, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
304 92 0.30
305 47 0.16
306 153 0.50
307 11 0.04
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (307 bp):
CATCATCAAAAACCATAAATCAAACCAAATGCTACTCTTCTTTACCCCCAATAAATTTCCAGCAA
TAAAGTTGGAAATAAAGTATGTATATGTATGGGATAAAACTATGGCAATGCTTTTGCATTCACAT
TTTATTTGAATTCTCCAGCTTCCTTTGTCACCCTCTGGGAAAATGAGATGGGAACCAAGCAAAGT
CCTCTACTTCTTAGATCTTGTTGCTTCCTTCCGATTTCCTGCTAAATAAATGCAATTTTATAAAA
TAAGATTTAAATTATACATTGTTACAATGAGGAATAAAAACCCAAAA
Found at i:149326 original size:14 final size:14
Alignment explanation
Indices: 149309--149369 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
149299 AAAAATGAAG
*
149309 AATAAAAATAAGTA
1 AATAAAAATAAATA
*
149323 AAT-AAAATAAAAA
1 AATAAAAATAAATA
*
149336 AAGAAAAATAAATA
1 AATAAAAATAAATA
149350 AATAAATAATAAATGA
1 AATAAA-AATAAAT-A
149366 AATA
1 AATA
149370 TAATATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
13 10 0.26
14 17 0.44
15 7 0.18
16 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:149337 original size:8 final size:8
Alignment explanation
Indices: 149280--149358 Score: 52
Period size: 9 Copynumber: 9.2 Consensus size: 8
149270 GTGTTAGAGG
149280 AAAAAAAT
1 AAAAAAAT
149288 GAAAAAAAT
1 -AAAAAAAT
*
149297 GAAAAAAT
1 AAAAAAAT
* *
149305 -GAAGAAT
1 AAAAAAAT
149312 AAAAATAAGT
1 AAAAA-AA-T
149322 AAATAAAAT
1 AAA-AAAAT
*
149331 AAAAAAAGA
1 AAAAAAA-T
149340 AAAATAAAT
1 AAAA-AAAT
*
149349 AAATAAAT
1 AAAAAAAT
149357 AA
1 AA
149359 TAAATGAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
7 5 0.09
8 19 0.34
9 21 0.38
10 9 0.16
11 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:149342 original size:27 final size:26
Alignment explanation
Indices: 149312--149377 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
149302 AATGAAGAAT
*
149312 AAAAATAAGTAAATAAAATAAAAAAAG
1 AAAAATAAATAAAT-AAATAAAAAAAG
* *
149339 AAAAATAAATAAATAAATAATAAATG
1 AAAAATAAATAAATAAATAAAAAAAG
*
149365 AAATATAATATAA
1 AAAAATAA-ATAA
149378 TATATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 17 0.50
27 17 0.50
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (26 bp):
AAAAATAAATAAATAAATAAAAAAAG
Found at i:149350 original size:4 final size:4
Alignment explanation
Indices: 149314--149379 Score: 50
Period size: 4 Copynumber: 16.2 Consensus size: 4
149304 TGAAGAATAA
*
149314 AAAT AAGT AAAT AAAAT AAA- AAA- AGAA- AAAT AAAT AAAT AAAT -AAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT
149360 AAAT GAAAT ATAAT ATAAT A
1 AAAT -AAAT A-AAT A-AAT A
149380 TATATATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
3 9 0.17
4 28 0.52
5 17 0.31
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:149432 original size:71 final size:69
Alignment explanation
Indices: 149332--149467 Score: 154
Period size: 69 Copynumber: 1.9 Consensus size: 69
149322 AAATAAAATA
* * *
149332 AAAAAAGAAAAATAAATAAATAAATAATAAATGAAATA-TAATAT-AATATATATATATATATAT
1 AAAAAAGAAAAATAAATAAATAAACAAT-AATG--ATAGTAATATGAAAATATA-ATATATATAA
149395 AAAAGAGT
62 AAAAGAGT
*
149403 AAAATAGAAAAAT-AAT-AATCATAACAATAATGATAGTAATATGAAAATATAATATATATAAAA
1 AAAAAAGAAAAATAAATAAAT-A-AACAATAATGATAGTAATATGAAAATATAATATATATAAAA
149466 AA
64 AA
149468 AAAAAAACAA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
68 3 0.05
69 22 0.39
70 15 0.26
71 17 0.30
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.27
Consensus pattern (69 bp):
AAAAAAGAAAAATAAATAAATAAACAATAATGATAGTAATATGAAAATATAATATATATAAAAAA
GAGT
Found at i:149621 original size:2 final size:2
Alignment explanation
Indices: 149614--149663 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
149604 ATAATTACAA
149614 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149655 AT AT AT AT A
1 AT AT AT AT A
149664 GTACGCTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:150283 original size:37 final size:37
Alignment explanation
Indices: 150242--150346 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
150232 GTGCTTGTGG
* *
150242 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * *
150279 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
150316 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
150347 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:151212 original size:106 final size:106
Alignment explanation
Indices: 151077--152217 Score: 1577
Period size: 106 Copynumber: 10.9 Consensus size: 106
151067 GCATTGTTCC
* * * ** *
151077 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * *
151142 CCAGTC-GTCCCTTCGTTGTGAAGTTGGAA-TTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTT-GAACTTGCGTTGTCTG
* * *
151183 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
151242 TCAGCCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
151284 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
151348 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
151389 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
151454 CCAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * * *
151495 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
151560 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
151601 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTATTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
151666 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
151707 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
151772 CCAGCGGTCCCTTAGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
151813 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
151878 CCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
151919 GAGTTCAATATCCTACCCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
151984 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
152025 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGACTCTG-AA-T--GAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
152086 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
152127 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGTCTCCGAAATT-GGAATATTG----TTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATTGTTTATTGACA
* * *
152187 A-CAGCCGTCCCTTCGT-TTAAAGTTGAACTTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
152218 TGTTCTTGAG
Statistics
Matches: 936, Mismatches: 83, Indels: 38
0.89 0.08 0.04
Matches are distributed among these distances:
99 5 0.01
100 86 0.09
101 18 0.02
102 104 0.11
103 2 0.00
104 5 0.01
105 10 0.01
106 704 0.75
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:152625 original size:18 final size:18
Alignment explanation
Indices: 152599--152634 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
152589 GTTGAATCCC
*
152599 CAAATAATGCCCCAATAT
1 CAAAAAATGCCCCAATAT
152617 CAAAAAATGCCCCAATAT
1 CAAAAAATGCCCCAATAT
152635 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.28, G:0.06, T:0.19
Consensus pattern (18 bp):
CAAAAAATGCCCCAATAT
Found at i:153067 original size:22 final size:22
Alignment explanation
Indices: 153041--153117 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
153031 TTATGTTTGG
153041 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
153063 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATGC
* *
153085 TCATAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
153107 TCAACGGTTTG
1 TCAAAGGTTTG
153118 ATGGGGTAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:153747 original size:16 final size:15
Alignment explanation
Indices: 153728--153808 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 15
153718 TTGTCCCTTT
153728 TTCTTTTGATTTTTTC
1 TTCTTTT-ATTTTTTC
* *
153744 TTCTTTTCTTTTTTG
1 TTCTTTTATTTTTTC
*
153759 TTC-TTGATTCTCTTT-
1 TTCTTTTATT-T-TTTC
153774 TT-TATTTATTTTTTGC
1 TTCT-TTTATTTTTT-C
*
153790 TTCTTTT-TTTTTTG
1 TTCTTTTATTTTTTC
153804 TTCTT
1 TTCTT
153809 GATTGGATCT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
14 12 0.23
15 19 0.37
16 20 0.38
17 1 0.02
ACGTcount: A:0.05, C:0.12, G:0.06, T:0.77
Consensus pattern (15 bp):
TTCTTTTATTTTTTC
Found at i:153749 original size:22 final size:22
Alignment explanation
Indices: 153724--153803 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 22
153714 CTTTTTGTCC
*
153724 CTTTTTCTTTTGATTTTTTCTT
1 CTTTTTTTTTTGATTTTTTCTT
153746 CTTTTCTTTTTTG-TTCTTGATTC-T
1 CTTTT-TTTTTTGATT-TT--TTCTT
*
153770 CTTTTTTATTT-ATTTTTTGCTT
1 CTTTTTTTTTTGATTTTTT-CTT
153792 CTTTTTTTTTTG
1 CTTTTTTTTTTG
153804 TTCTTGATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
20 2 0.04
21 1 0.02
22 20 0.43
23 15 0.32
24 6 0.13
25 3 0.06
ACGTcount: A:0.05, C:0.12, G:0.06, T:0.76
Consensus pattern (22 bp):
CTTTTTTTTTTGATTTTTTCTT
Found at i:156668 original size:2 final size:2
Alignment explanation
Indices: 156661--156689 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
156651 TGAAATATTA
156661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
156690 AATGAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:160293 original size:32 final size:31
Alignment explanation
Indices: 160257--160329 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
160247 TAACGAATCG
* *
160257 GTTGATTTTCGGTTCGTATCAATATTGGATCA
1 GTTGATTTT-GGATCGGATCAATATTGGATCA
* *
160289 GTTGAATTTTTGATCGGGTCAATATTGGATCA
1 GTTG-ATTTTGGATCGGATCAATATTGGATCA
160321 GTTGATTTT
1 GTTGATTTT
160330 TAGGTCGGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 5 0.14
32 26 0.72
33 5 0.14
ACGTcount: A:0.22, C:0.10, G:0.23, T:0.45
Consensus pattern (31 bp):
GTTGATTTTGGATCGGATCAATATTGGATCA
Found at i:160338 original size:32 final size:32
Alignment explanation
Indices: 160275--160394 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 32
160265 TCGGTTCGTA
*
160275 TCAATATTGGATCAGTTGAATTTTT-GATCGGG
1 TCAATATTGGATCAGTTG-ATTTTTAGGTCGGG
160307 TCAATATTGGATCAGTTGATTTTTAGGTCGGG
1 TCAATATTGGATCAGTTGATTTTTAGGTCGGG
* **** * *
160339 TTAATACCATATCGGTTAGA-TTTCAGGTCGGG
1 TCAATATTGGATCAGTT-GATTTTTAGGTCGGG
* *
160371 TCAATATAGGATCAATTGATTTTT
1 TCAATATTGGATCAGTTGATTTTT
160395 GGTTTAGATT
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
31 8 0.12
32 59 0.86
33 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (32 bp):
TCAATATTGGATCAGTTGATTTTTAGGTCGGG
Found at i:162788 original size:23 final size:23
Alignment explanation
Indices: 162762--162830 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
162752 CACCACAGCT
*
162762 CGTATAAATGCACCGAAGTACCA
1 CGTAGAAATGCACCGAAGTACCA
* * *
162785 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTACCA
*
162808 CGTAGAAAAGCACCGAAGTACCA
1 CGTAGAAATGCACCGAAGTACCA
162831 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTACCA
Found at i:163292 original size:2 final size:2
Alignment explanation
Indices: 163285--163309 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
163275 TCATCTTCCT
163285 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
163310 CATTTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:164530 original size:64 final size:64
Alignment explanation
Indices: 164421--164582 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
164411 TTCCCTTGAA
* * * * *
164421 GTGCATCGATGCACTACTCATGCGTCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
** * ** *
164485 GTGCATCGATGCACTCCTTATGCATCGATGTACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
164549 GTGCATCGATGCACTTCC-TATGCATCGATACACA
1 GTGCATCGATGCAC-TCCTTATGCATCGATACACA
164583 CTGAATAATT
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 73 0.89
65 9 0.11
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:166964 original size:20 final size:20
Alignment explanation
Indices: 166939--166986 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
166929 GAAGAACAAA
166939 TATCGATATTATCCTGATAG
1 TATCGATATTATCCTGATAG
166959 TATCGATATTATCCTGATAG
1 TATCGATATTATCCTGATAG
166979 TATCGATA
1 TATCGATA
166987 CTCTACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TATCGATATTATCCTGATAG
Found at i:169605 original size:20 final size:20
Alignment explanation
Indices: 169560--169653 Score: 124
Period size: 20 Copynumber: 4.9 Consensus size: 20
169550 TGAATATTTA
169560 TCCCGAAGGACCACT-A-TG
1 TCCCGAAGGACCACTGATTG
169578 TCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACTGATTG
* *
169598 TTCCGAAGAACCACT-A-TG
1 TCCCGAAGGACCACTGATTG
* *
169616 TCCTGAAGGACCACTGTTTG
1 TCCCGAAGGACCACTGATTG
169636 TCCCGAAGGACCACTGAT
1 TCCCGAAGGACCACTGAT
169654 AATCCCTCGA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
18 29 0.45
19 2 0.03
20 33 0.52
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (20 bp):
TCCCGAAGGACCACTGATTG
Found at i:169605 original size:38 final size:38
Alignment explanation
Indices: 169560--169650 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
169550 TGAATATTTA
169560 TCCCGAAGGACCACTATGTCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACTATGTCCCGAAGGACCACTGATTG
* * * *
169598 TTCCGAAGAACCACTATGTCCTGAAGGACCACTGTTTG
1 TCCCGAAGGACCACTATGTCCCGAAGGACCACTGATTG
169636 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
169651 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.21
Consensus pattern (38 bp):
TCCCGAAGGACCACTATGTCCCGAAGGACCACTGATTG
Found at i:170621 original size:18 final size:17
Alignment explanation
Indices: 170591--170624 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
170581 TATCATCTTC
170591 TTATATAATCATATGAA
1 TTATATAATCATATGAA
170608 TTATATATATCATATGA
1 TTATATA-ATCATATGA
170625 TTTACTACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (17 bp):
TTATATAATCATATGAA
Found at i:172849 original size:14 final size:14
Alignment explanation
Indices: 172830--172859 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
172820 TTGATCTTTT
172830 AAGTTTTATTAAGA
1 AAGTTTTATTAAGA
*
172844 AAGTTTTATTGAGA
1 AAGTTTTATTAAGA
172858 AA
1 AA
172860 CTCAATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (14 bp):
AAGTTTTATTAAGA
Done.